The Manchester United forward stepped up to score from the spot in the 59th minute to draw the hosts level - just one minute after a Jordan Henderson own goal had given the visitors the lead - handing the 29-year old his 44th internaional strike to become the joint third-highest England goalscorer of all time.
The hosts soon took advantage of that momentum and took the lead just seven minutes later courtesy of Danny Welbeck's tap in, before the Arsenal striker capped off the win by doubling his tally six minutes later following some good work from Raheem Sterling.
The win preserves England's 100 per cent start to their Euro 2016 qualifying campaign, while Slovenia are now level on points with Switzerland, who ran out 4-0 winners over Lithuania after scoring four goals in the final 24 minutes.
The hosts took the lead courtesy of a Giedrius Arlauskis own goal on 68 minutes, before Fabian Schar doubled the lead seconds later.
A late brace from Xherdan Shaqiri wrapped up the win, which leaves the Swiss firmly in touch with the Group E summit.
Bottom side San Marino made history with a shock 0-0 draw at home to Estonia to earn their first ever point in a UEFA Euro 2016 qualifying campaign and only their fourth competitive clean sheet.
Another side to cause a stir were Liechtenstein, who secured a shock of their own in the form of a 1-0 win over Moldova.
A superb second-half free-kick from captain Franz Burgmeier was enough to hand the visitors victory, their first since 2012.
At the top of Group G, Austria ended Russia's unbeaten run with a well-earned 1-0 win in Vienna.
Rubin Okotie, the 1860 Munich striker, came off the bench to seal the win 17 minutes from time, turning in a Martin Harnik cross in from close range, preserving his side's unbeaten start to the campaign.
The result leaves Marcel Koller's side four points clear of nearest rivals Sweden, who were held to a 1-1 draw by Montenegro.
In Group C, a stunning strike from Isco managed to inspire Spain to a comfortable 3-0 win over Belarus in the first international match to be held at the Estadio Nuevo Colombino.
The Real Madrid star was on hand after 18 minutes to curl home a superb 30-yard strike, before goals from Sergio Busquets and Pedro wrapped up the win.
The win leaves Vicente del Bosque's side level on points with Ukraine, who secured a routine 3-0 win away to Luxembourg.
However, Slovakia continue to top the group after securing a fourth straight win with a 2-0 victory away to Macedonia, leaving them three points clear of Spain at the top.
